[BioRuby] Alignment plugin

Pjotr Prins pjotr.public14 at thebird.nl
Mon Apr 26 14:52:03 UTC 2010

On Mon, Apr 26, 2010 at 02:03:35PM +0100, Rutger Vos wrote:
> Do you feel that these objects could/should also double as
> character-state matrices?

Yes. Rather than hacking a matrix on top of a sequence alignment -
what I want to do is:

A sequence is a list of nucleotides/aminoacid/degenerates (whatever).

Each sequence has a name and other properties (like gaps).

Each nucleotide/aminoacid has properties by itself. Do gaps have

A 'column' may have properties.

Any type of matrix can be derived from the internal structure. I
don't think the underlying storage pattern is a matrix.

Something else, I want sequence storage to be transparently open to
other back-ends. I.e.  memory storage, SQL storage, other storage etc.
I want to get away from storing everything in memory. With big data
it is simply not a great idea (though not so relevant for alignments,


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